Record all variants found, rather than the first in the for loop.

[Phelimb]

  if ( (I==Resistant) || (I==MixedInfection) ) 
{
  update_called_variants(called_variants,i,abi->vars[i]);
  return I;
}

This breaks the loop through all variants if it hits one, so we only ever say we see one variant when, in fact, there may be more than one there.

[iqbal-lab]

I suggest we don't do this til after submission.

[iqbal-lab]

This is done I believe